New Analysis Promises to Speed Application of Human
Genome Draft

By Joanna DownerJohns Hopkins Medicine

A small team of scientists has dramatically improved
"gene chip" technology, for the first time making it a
practical method for rapidly determining the sequence of
genetic building blocks. The advance, likely to speed the
search for disease-related genetic changes, is reported in
the November issue of the journal Genome Research.

The gene chips, or microarrays, are dotted with a
microscopic grid of hundreds of thousands of tiny segments
of DNA determined by the Human Genome Project. These
segments, fixed in known spots on the chip, find their
matches in a sample of DNA. The better the match, the more
likely the known DNA sequence reflects the unknown sample
sequence, explains the team from the Johns Hopkins School of
Medicine and a biotechnology company, Affymetrix, Inc.

A new analysis method lets the team identify and focus
on the chips' more reliable information. "Until now, ways to
analyze the chips were unable to distinguish highly accurate
data from less reliable information," says lead author David
Cutler, a research associate in the university's
McKusick-Nathans Institute of Genetic Medicine.

"We need the chips to be very accurate because
variation in the human genome is relatively rare," adds
Michael Zwick, John Wasmuth postdoctoral fellow in the
McKusick-Nathans Institute. "We've taken advantage of the
fact that individual features, individual points, can be
very reliable. Our analysis technique identifies them."

Previously, the only way to figure out the order of
building blocks, or bases, in genetic material was to use
machines known as DNA sequencers, which is still the only
way to obtain the first genome of a species. Microarrays had
been useful to study gene activity but not gene sequence,
Cutler says.

"We took the most logical, straightforward approach we
could to help us determine which of the microarray sequences
to pay attention to and which ones to ignore," Cutler adds.
"Our system actually evaluates and scores the reliability of
each individual building block."

Using gene chips and their new analysis, the scientists
were able to accurately determine the order of 2 million
blocks of each of 40 individuals' genomes in just a year, a
fraction of the time required by traditional technology. The
parts of the human genome carrying instructions for proteins
consist of about 45 million bases, while the whole genome is
around 3 billion bases.

There's so little natural variability in human DNA that
an analysis that is 99.9 percent accurate isn't good enough,
Zwick says. Such an analysis would give 10 errors out of
every 10,000 points in the sequence, but the natural
variability in the human genome is only eight in 10,000. "To
be useful, the data has to have fewer than eight errors in
10,000," he explains.

The new technique identified more than 80 percent of
the determined sequences as 99.9999 percent accurate, making
it possible to search those regions for changes that might
be linked to diseases such as high blood pressure and
schizophrenia, say the researchers, who will make their
analysis tool available to others.

"Technology has advanced to where we can get lots of
data about both gene expression and gene sequences," says
Aravinda Chakravarti, director of the McKusick-Nathans
Institute. "We can use these techniques to examine diseases
that seem functionally similar but on a genetic level are
not."

The study was funded by the National Institutes of
Health. The other authors are Christopher Yohn, Katherine
Tobin and Carl Kashuk of the McKusick-Nathans Institute of
Genetic Medicine at Johns Hopkins; Minerva Carrasquillo,
Debra Mathews and Evan Eichler of Case Western Reserve
University; and Nila Shah and Janet Warrington of
Affymetrix, Inc., Santa Clara, Calif.